@fnndsc/salsa 3.14.0 → 3.16.0

package/dist/dicom/tags.d.ts

@@ -0,0 +1,80 @@
+import { type Result } from '@fnndsc/cumin';
+import { type DicomTagGroup } from './dictionary.js';
+/** One element of a DICOM dataset, as every surface sees it. */
+export interface DicomTag {
+    /** `(gggg,eeee)`, upper-case hex. */
+    tag: string;
+    /** Dictionary name; `PrivateTag` or `Unknown` when the dictionary has none. */
+    name: string;
+    vr: string;
+    /** The value in text. Multi-valued elements join with `\`; bulk data reads `<N bytes>`. */
+    value: string;
+    group: DicomTagGroup;
+    /** True when the tag identifies a person or an institution. */
+    phi: boolean;
+    /** Words for a coded value, when the kernel knows them. */
+    decoded?: string;
+    /** Sequence items, each a dataset of its own. */
+    items?: DicomTag[][];
+}
+/** Everything read from one file. */
+export interface DicomTagSet {
+    tags: DicomTag[];
+    /** From the file meta group; absent for a bare dataset. */
+    transferSyntaxUID?: string;
+}
+/** A tag whose value changes across a folder. */
+export interface DicomVaryingTag {
+    tag: string;
+    name: string;
+    vr: string;
+    group: DicomTagGroup;
+    phi: boolean;
+    /** How many distinct values the folder holds. */
+    distinct: number;
+    /** The value in the first file, in folder order. */
+    first: string;
+    /** The value in the last file, in folder order. */
+    last: string;
+    /** Every file's value, in folder order. Files without the tag carry `null`. */
+    values: Array<{
+        path: string;
+        value: string | null;
+    }>;
+}
+/** What a folder of files shares and what changes across it. */
+export interface DicomTagsSummary {
+    constant: DicomTag[];
+    varying: DicomVaryingTag[];
+}
+/**
+ * Reads the elements of a DICOM file.
+ *
+ * @param bytes - The whole file, Part 10 header included.
+ * @returns The tag set, or an error when the bytes are not a DICOM file.
+ */
+export declare function dicomTags_read(bytes: Buffer): Result<DicomTagSet>;
+/**
+ * Finds one tag by name in a tag set's top level.
+ *
+ * @param tags - The tags to search.
+ * @param name - The dictionary name.
+ * @returns The tag, or undefined.
+ */
+export declare function dicomTag_find(tags: DicomTag[], name: string): DicomTag | undefined;
+/**
+ * Tells constant from varying across a folder's files, in folder order.
+ *
+ * A tag is constant when every file carries it with the same value
+ * (sequences compare by their items). Anything else, including a tag some
+ * files lack, is varying, with its first and last value and its distinct
+ * count. Files that failed to read are the caller's to report; they are not
+ * passed here.
+ *
+ * @param files - Each file's path and tag set, in folder order.
+ * @returns The summary.
+ */
+export declare function dicomTags_summarize(files: Array<{
+    path: string;
+    tags: DicomTagSet;
+}>): DicomTagsSummary;

package/dist/dicom/tags.js

@@ -0,0 +1,234 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.dicomTags_read = dicomTags_read;
+exports.dicomTag_find = dicomTag_find;
+exports.dicomTags_summarize = dicomTags_summarize;
+/**
+ * @file DICOM tag reading: one parser for every surface.
+ *
+ * A DICOM file is a dictionary of elements. Reading one here gives every
+ * surface the same answer: the tag, its dictionary name and VR, its value in
+ * text, the module it belongs to, whether it identifies someone, and words
+ * for the coded values a reader meets first. Sequences keep their items.
+ * Across a folder, the same reader tells constant from varying: what the
+ * series shares against what changes slice by slice.
+ *
+ * Bulk values (pixel data and friends) are never rendered as bytes; the
+ * listing says how many bytes there were. Long text is carried whole on the
+ * model; a surface that bounds it says so.
+ *
+ * @module
+ */
+const dcmjs_1 = __importDefault(require("dcmjs"));
+const cumin_1 = require("@fnndsc/cumin");
+const dictionary_js_1 = require("./dictionary.js");
+/** VRs whose values are bulk bytes, never text. */
+const BULK_VRS = new Set(['OB', 'OW', 'OF', 'OD', 'OL', 'OV', 'UN']);
+/** Group numbers whose every element is a sequence item boundary or padding. */
+const STRUCTURAL_TAGS = new Set(['FFFEE000', 'FFFEE00D', 'FFFEE0DD']);
+/**
+ * Reads the elements of a DICOM file.
+ *
+ * @param bytes - The whole file, Part 10 header included.
+ * @returns The tag set, or an error when the bytes are not a DICOM file.
+ */
+function dicomTags_read(bytes) {
+    const buffer = new Uint8Array(bytes).slice().buffer;
+    try {
+        const message = dcmjs_1.default.data.DicomMessage.readFile(buffer, { ignoreErrors: true });
+        const meta = dict_flatten(message.meta);
+        const body = dict_flatten(message.dict);
+        const syntax = meta.find((tag) => tag.name === 'TransferSyntaxUID');
+        return (0, cumin_1.Ok)({
+            tags: [...meta, ...body],
+            ...(syntax !== undefined ? { transferSyntaxUID: syntax.value } : {}),
+        });
+    }
+    catch {
+        return (0, cumin_1.Err)();
+    }
+}
+/**
+ * Turns a raw dictionary into tags, in tag order, sequences nested.
+ *
+ * @param dict - A dcmjs dictionary keyed by `ggggeeee`.
+ * @returns The tags.
+ */
+function dict_flatten(dict) {
+    const keys = Object.keys(dict)
+        .filter((key) => /^[0-9A-Fa-f]{8}$/.test(key) && !STRUCTURAL_TAGS.has(key.toUpperCase()))
+        .sort();
+    return keys.map((key) => element_toTag(key, dict[key]));
+}
+/**
+ * Renders one element as a tag.
+ *
+ * @param key - The `ggggeeee` key.
+ * @param element - The raw element.
+ * @returns The tag.
+ */
+function element_toTag(key, element) {
+    const upper = key.toUpperCase();
+    const tag = `(${upper.slice(0, 4)},${upper.slice(4)})`;
+    const groupNumber = parseInt(upper.slice(0, 4), 16);
+    const entry = dcmjs_1.default.data.DicomMetaDictionary.dictionary[tag];
+    const isPrivate = groupNumber % 2 === 1;
+    const name = entry?.name ?? (isPrivate ? 'PrivateTag' : 'Unknown');
+    const vr = element.vr || entry?.vr || 'UN';
+    const values = element.Value ?? [];
+    const result = {
+        tag,
+        name,
+        vr,
+        value: '',
+        group: (0, dictionary_js_1.tagGroup_of)(groupNumber, entry?.name),
+        phi: dictionary_js_1.DICOM_PHI_TAGS.has(name),
+    };
+    if (vr === 'SQ') {
+        const items = values.map((item) => dict_flatten(item));
+        result.items = items;
+        result.value = `${items.length} item${items.length === 1 ? '' : 's'}`;
+        return result;
+    }
+    if (BULK_VRS.has(vr)) {
+        result.value = `<${bulk_bytes(values)} bytes>`;
+        return result;
+    }
+    result.value = values.map((value) => value_text(value, vr)).join('\\');
+    const decoded = decoded_of(name, result.value);
+    if (decoded !== undefined)
+        result.decoded = decoded;
+    return result;
+}
+/**
+ * Sums the bytes of a bulk value list.
+ *
+ * @param values - Buffers or typed arrays.
+ * @returns Total byte length.
+ */
+function bulk_bytes(values) {
+    let total = 0;
+    for (const value of values) {
+        if (value instanceof ArrayBuffer)
+            total += value.byteLength;
+        else if (ArrayBuffer.isView(value))
+            total += value.byteLength;
+    }
+    return total;
+}
+/**
+ * One value in text. Person names are alphabetic components; everything
+ * else is its string form.
+ *
+ * @param value - The raw value.
+ * @param vr - The element's VR.
+ * @returns The text.
+ */
+function value_text(value, vr) {
+    if (vr === 'PN' && value !== null && typeof value === 'object') {
+        const parts = value;
+        return String(parts.Alphabetic ?? parts.Ideographic ?? parts.Phonetic ?? '');
+    }
+    if (value === null || value === undefined)
+        return '';
+    return String(value);
+}
+/**
+ * Words for a coded value: the short dictionary list, plus SOP class UIDs
+ * named through dcmjs.
+ *
+ * @param name - The tag's name.
+ * @param value - The tag's text value.
+ * @returns Words, or nothing.
+ */
+function decoded_of(name, value) {
+    if (name === 'SOPClassUID' || name === 'MediaStorageSOPClassUID') {
+        return dcmjs_1.default.data.DicomMetaDictionary.sopClassNamesByUID[value];
+    }
+    return (0, dictionary_js_1.tagValue_decode)(name, value);
+}
+/**
+ * Finds one tag by name in a tag set's top level.
+ *
+ * @param tags - The tags to search.
+ * @param name - The dictionary name.
+ * @returns The tag, or undefined.
+ */
+function dicomTag_find(tags, name) {
+    return tags.find((tag) => tag.name === name);
+}
+/**
+ * Tells constant from varying across a folder's files, in folder order.
+ *
+ * A tag is constant when every file carries it with the same value
+ * (sequences compare by their items). Anything else, including a tag some
+ * files lack, is varying, with its first and last value and its distinct
+ * count. Files that failed to read are the caller's to report; they are not
+ * passed here.
+ *
+ * @param files - Each file's path and tag set, in folder order.
+ * @returns The summary.
+ */
+function dicomTags_summarize(files) {
+    const order = [];
+    const byTag = new Map();
+    for (const file of files) {
+        const seen = new Map();
+        for (const tag of file.tags.tags) {
+            if (!byTag.has(tag.tag)) {
+                byTag.set(tag.tag, new Map());
+                order.push(tag.tag);
+            }
+            seen.set(tag.tag, tag);
+        }
+        for (const [key, tag] of seen)
+            byTag.get(key).set(file.path, tag);
+    }
+    const constant = [];
+    const varying = [];
+    for (const key of order.sort()) {
+        const perFile = byTag.get(key);
+        const values = files.map((file) => {
+            const tag = perFile.get(file.path);
+            return { path: file.path, value: tag === undefined ? null : tag_comparable(tag) };
+        });
+        const distinctValues = new Set(values.map((entry) => entry.value));
+        const sample = perFile.values().next().value;
+        if (distinctValues.size === 1 && !distinctValues.has(null)) {
+            constant.push(sample);
+            continue;
+        }
+        const present = values.filter((entry) => entry.value !== null);
+        varying.push({
+            tag: sample.tag,
+            name: sample.name,
+            vr: sample.vr,
+            group: sample.group,
+            phi: sample.phi,
+            distinct: distinctValues.size - (distinctValues.has(null) ? 1 : 0),
+            first: present[0].value,
+            last: present[present.length - 1].value,
+            values: values.map((entry) => ({
+                path: entry.path,
+                value: entry.value === null ? null : perFile.get(entry.path).value,
+            })),
+        });
+    }
+    return { constant, varying };
+}
+/**
+ * The value a tag is compared by across files: its text, or for a sequence
+ * the text of its items.
+ *
+ * @param tag - The tag.
+ * @returns A comparable string.
+ */
+function tag_comparable(tag) {
+    if (tag.items === undefined)
+        return tag.value;
+    return JSON.stringify(tag.items.map((item) => item.map((inner) => `${inner.tag}=${tag_comparable(inner)}`)));
+}
+//# sourceMappingURL=tags.js.map

package/dist/dicom/tags.js.map

@@ -0,0 +1 @@
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package/dist/files/index.js

@@ -364,6 +364,15 @@ async function files_getGroup(assetName, path) {
         const fileContext = await cumin_1.chrisContext.current_get(cumin_1.Context.ChRISfolder);
         path = fileContext ? fileContext : "/";
     }
+    // A projection path (/proc, /net/pacs, /etc, /usr/share, or an ancestor of
+    // one) has no CUBE folder of files behind it: its provider lists it. Asking
+    // cumin to build a folder context for it cannot succeed, and a path walk
+    // that visits every ancestor — `cd` resolving a /proc job's links, a
+    // listing probing parents — turns that failure into a wall of identical
+    // errors. The group a projection would answer with is no group at all.
+    if (dispatcher_js_1.vfsDispatcher.path_isVirtual(path)) {
+        return null;
+    }
     let chrisFileSystemGroup = null;
     try {
         switch (assetName) {

package/dist/files/index.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -10,6 +10,7 @@ export * from './context/index.js';
 export * from './store/index.js';
 export * from './pipelines/index.js';
 export * from './pacs/index.js';
+export * from './dicom/index.js';
 export * from './retrieve/watch.js';
 export * from './vfs/index.js';
 export * from './tags/index.js';

package/dist/index.js

@@ -27,6 +27,7 @@ __exportStar(require("./context/index.js"), exports);
 __exportStar(require("./store/index.js"), exports);
 __exportStar(require("./pipelines/index.js"), exports);
 __exportStar(require("./pacs/index.js"), exports);
+__exportStar(require("./dicom/index.js"), exports);
 __exportStar(require("./retrieve/watch.js"), exports);
 __exportStar(require("./vfs/index.js"), exports);
 __exportStar(require("./tags/index.js"), exports);

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAAA;;;GAGG;;;;;;;;;;;;;;;;;AAEH,mDAAiC;AACjC,qDAAmC;AACnC,mDAAiC;AACjC,qDAAmC;AACnC,qDAAmC;AACnC,mDAAiC;AACjC,uDAAqC;AACrC,kDAAgC;AAChC,sDAAoC;AACpC,iDAA+B;AAC/B,kDAAgC;AAChC,oDAAkC;AAClC,yDAAuC;AACvC,6DAA2C;AAC3C,uDAAqC;AACrC,qDAAmC;AACnC,kDAAgC;AAChC,mDAAiC;AACjC,mDAAygB;AAAhgB,4GAAA,iBAAiB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAAE,qHAAA,0BAA0B,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAA8B,0GAAA,eAAe,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,yGAAA,cAAc,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,iHAAA,sBAAsB,OAAA;AAEve,mDAAwE;AAA/D,+GAAA,eAAe,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAE3C,mDAAyE;AAAhE,gHAAA,gBAAgB,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAC5C,iDAAyD;AAAhD,mHAAA,oBAAoB,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAAA;;;GAGG;;;;;;;;;;;;;;;;;AAEH,mDAAiC;AACjC,qDAAmC;AACnC,mDAAiC;AACjC,qDAAmC;AACnC,qDAAmC;AACnC,mDAAiC;AACjC,uDAAqC;AACrC,kDAAgC;AAChC,mDAAiC;AACjC,sDAAoC;AACpC,iDAA+B;AAC/B,kDAAgC;AAChC,oDAAkC;AAClC,yDAAuC;AACvC,6DAA2C;AAC3C,uDAAqC;AACrC,qDAAmC;AACnC,kDAAgC;AAChC,mDAAiC;AACjC,mDAAygB;AAAhgB,4GAAA,iBAAiB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAAE,qHAAA,0BAA0B,OAAA;AAAE,sHAAA,2BAA2B,OAAA;AAAE,gHAAA,qBAAqB,OAAA;AAA8B,0GAAA,eAAe,OAAA;AAAE,6GAAA,kBAAkB,OAAA;AAAE,yGAAA,cAAc,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,+GAAA,oBAAoB,OAAA;AAAE,0GAAA,eAAe,OAAA;AAAE,8GAAA,mBAAmB,OAAA;AAAE,iHAAA,sBAAsB,OAAA;AAEve,mDAAwE;AAA/D,+GAAA,eAAe,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAE3C,mDAAyE;AAAhE,gHAAA,gBAAgB,OAAA;AAAE,iHAAA,iBAAiB,OAAA;AAC5C,iDAAyD;AAAhD,mHAAA,oBAAoB,OAAA"}

package/dist/retrieve/watch.d.ts

@@ -26,6 +26,9 @@ export type RetrieveProgressStatus = 'running' | 'done' | 'unconfirmed' | 'error
  * @property actualFiles - Most recent file count from LONK progress updates.
  * @property lastProgressFiles - `actualFiles` at the last progress tick (stall detection).
  * @property lastProgressTime - Timestamp of the last progress tick.
+ * @property firstFileTime - When this series' first file arrived; 0 while it
+ *   is still waiting its turn. The long stop counts from here, so a series
+ *   queued behind a dozen others is not charged for the wait.
  * @property startTime - Timestamp when the retrieve was fired.
  * @property lonkConfirmed - True only after an explicit LONK `done` or a storage confirmation.
  * @property cubePathDir - CUBE folder the series landed in (resolved post-pull).
@@ -42,6 +45,7 @@ export interface RetrieveTask {
     actualFiles: number;
     lastProgressFiles: number;
     lastProgressTime: number;
+    firstFileTime: number;
     startTime: number;
     lonkConfirmed: boolean;
     cubePathDir: string | null;

package/dist/retrieve/watch.js

@@ -62,6 +62,7 @@ function retrieveTask_make(info) {
         actualFiles: 0,
         lastProgressFiles: 0,
         lastProgressTime: Date.now(),
+        firstFileTime: 0,
         startTime: 0,
         lonkConfirmed: false,
         cubePathDir: null,
@@ -240,6 +241,11 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
     await new Promise((resolve) => {
         let resolved = false;
         let reconnectsLeft = WATCH_RECONNECT_ATTEMPTS;
+        // When this watch last saw life from the PACS, on ANY of its series.
+        // Quiet is a property of the watch, not of each series: a PACS busy
+        // sending the first series has not gone silent on the ten queued
+        // behind it, and they cannot report files they have not been sent yet.
+        let lastActivityAt = Date.now();
         const done = () => {
             if (resolved)
                 return;
@@ -290,6 +296,9 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
                     return;
                 }
                 ws = replacement;
+                // A reconnection is a new view, not new silence: charging the
+                // gap to the PACS would declare the study dead on reconnect.
+                lastActivityAt = Date.now();
                 socket_listen();
             })
                 .catch(() => socket_replace());
@@ -302,17 +311,27 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
                     continue;
                 }
                 allTerminal = false;
-                if (t.startTime > 0 && now - t.startTime > SERIES_TIMEOUT_MS) {
-                    t.status = 'timeout';
-                    emit(t, 'timeout');
-                    continue;
-                }
+                // A series that began and then stopped is stalled on its own
+                // evidence: it was being sent, and it no longer is.
                 if (t.actualFiles > 0 && now - t.lastProgressTime > STALL_TIMEOUT_MS) {
                     t.status = 'stalled';
                     emit(t, 'stalled');
                     continue;
                 }
-                if (t.startTime > 0 && t.actualFiles === 0 && now - t.startTime > NO_ACTIVITY_TIMEOUT_MS) {
+                // The long stop: a series that trickles and never ends. Counted
+                // from its first file, never from the fire, so waiting a turn in a
+                // large study costs a series nothing.
+                if (t.firstFileTime > 0 && now - t.firstFileTime > SERIES_TIMEOUT_MS) {
+                    t.status = 'timeout';
+                    emit(t, 'timeout');
+                    continue;
+                }
+                // Nothing has arrived for this series. That is evidence of a lost
+                // retrieve only when nothing has arrived for ANY of them. Charged
+                // per series from its own fire time, this declared every series
+                // after the first few dead fifteen seconds into any study large
+                // enough that the PACS served them in turn.
+                if (t.startTime > 0 && t.actualFiles === 0 && now - lastActivityAt > NO_ACTIVITY_TIMEOUT_MS) {
                     t.status = 'pulled';
                     t.lonkConfirmed = false;
                     emit(t, 'unconfirmed');
@@ -334,11 +353,14 @@ async function retrieve_fireAndWatch(tasks, pacsserver, client, events = {}, pha
                     const t = taskByUID.get(seriesUID);
                     if (!t)
                         return;
+                    lastActivityAt = Date.now();
                     if ('ndicom' in message && typeof message.ndicom === 'number') {
                         const n = message.ndicom;
                         t.actualFiles = n;
                         t.lastProgressFiles = n;
                         t.lastProgressTime = Date.now();
+                        if (t.firstFileTime === 0 && n > 0)
+                            t.firstFileTime = t.lastProgressTime;
                         if (t.status === 'pending')
                             t.status = 'pulling';
                         emit(t, 'running');
@@ -410,6 +432,7 @@ async function retrieve_confirmLoop(allTasks, retryMax, pacsserver, client, even
             t.actualFiles = 0;
             t.lastProgressFiles = 0;
             t.lastProgressTime = Date.now();
+            t.firstFileTime = 0;
             t.startTime = 0;
             t.lonkConfirmed = false;
             t.syntheticQueryId = null;

package/dist/retrieve/watch.js.map

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package/dist/vfs/dispatcher.d.ts

@@ -43,6 +43,26 @@ export declare class VFSDispatcher {
      * @returns The matching VFSProvider or the default native provider.
      */
     provider_get(pathStr: string): VFSProvider;
+    /**
+     * Whether a path belongs to a projection rather than a real CUBE folder.
+     *
+     * A projection root (`/proc`, `/net/pacs`, `/etc`, `/usr/share`) is served
+     * by its own provider and has no folder of files behind it. Three shapes
+     * count as virtual: a path a non-native provider owns (at or under its
+     * prefix), and a path that is a strict ancestor of such a prefix (`/proc`
+     * above `/proc/jobs`, `/net` above `/net/pacs`) — its only children are
+     * the projections beneath it. The real root `/` is never virtual: it is
+     * the CUBE store's own root, which the native provider lists.
+     *
+     * The point of the question is to keep the raw CUBE-files layer from
+     * being asked to build a folder context for a path that has none — the
+     * request cannot succeed and only litters the error log, once per
+     * ancestor a path walk visits.
+     *
+     * @param pathStr - The absolute (or root-relative) path to classify.
+     * @returns True when a projection owns or is owned by the path.
+     */
+    path_isVirtual(pathStr: string): boolean;
     /**
      * Dispatches directory listing to matched provider.
      * Supports dynamic intermediate parent path synthesis for virtual prefixes.